Publications by authors named "Alexandre M Bonvin"

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The SH protein of mumps virus is a druggable pentameric viroporin.
Kira Devantier, Trine L Toft-Bertelsen, Andreas Prestel, Viktoria M S Kjær, Cagla Sahin, Alexandre Mjj Bonvin

Sci Adv· June 2025

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A novel antifolate suppresses growth of FPGS-deficient cells and overcomes methotrexate resistance.
Felix van der Krift, Dick W Zijlmans, Rhythm Shukla, Ali Javed, Panagiotis I Koukos, Alexandre Mjj Bonvin

Life Sci Alliance· November 2023

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PRODIGY-crystal: a web-tool for classification of biological interfaces in protein complexes.
Brian Jiménez-García, Katarina Elez, Panagiotis I Koukos, Alexandre Mjj Bonvin, Anna Vangone

Bioinformatics· November 2019

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Information-Driven, Ensemble Flexible Peptide Docking Using HADDOCK.
Cunliang Geng, Siddarth Narasimhan, João P G L M Rodrigues, Alexandre M J J Bonvin

Methods Mol Biol· February 2018

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A benchmark testing ground for integrating homology modeling and protein docking.
Tanggis Bohnuud, Lingqi Luo, Shoshana J Wodak, Alexandre M J J Bonvin, Zhiping Weng

Proteins· January 2017

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Prevention of Vγ9Vδ2 T Cell Activation by a Vγ9Vδ2 TCR Nanobody.
Renée C G de Bruin, Anita G M Stam, Anna Vangone, Paul M P van Bergen En Henegouwen, Henk M W Verheul, Alexandre M J J Bonvin

J Immunol· January 2017

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Molecular dynamics characterization of the conformational landscape of small peptides: A series of hands-on collaborative practical sessions for undergraduate students.
João P G L M Rodrigues, Adrien S J Melquiond, Alexandre M J J Bonvin

Biochem Mol Biol Educ· December 2016

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PRODIGY: a web server for predicting the binding affinity of protein-protein complexes.
Li C Xue, João Pglm Rodrigues, Panagiotis L Kastritis, Alexandre Mjj Bonvin, Anna Vangone

Bioinformatics· December 2016

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Structural basis of GM-CSF and IL-2 sequestration by the viral decoy receptor GIF.
Jan Felix, Eaazhisai Kandiah, Steven De Munck, Yehudi Bloch, Gydo C P van Zundert, Alexandre M J J Bonvin

Nat Commun· November 2016

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Structure of the bacterial plant-ferredoxin receptor FusA.
Rhys Grinter, Inokentijs Josts, Khedidja Mosbahi, Aleksander W Roszak, Richard J Cogdell, Alexandre M J J Bonvin

Nat Commun· October 2016

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Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment.
Marc F Lensink, Sameer Velankar, Andriy Kryshtafovych, Shen-You Huang, Dina Schneidman-Duhovny, Alexandre M J J Bonvin

Proteins· September 2016

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dMM-PBSA: A New HADDOCK Scoring Function for Protein-Peptide Docking.
Dimitrios Spiliotopoulos, Panagiotis L Kastritis, Adrien S J Melquiond, Alexandre M J J Bonvin, Giovanna Musco

Front Mol Biosci· September 2016

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New Insight into the Catalytic Mechanism of Bacterial MraY from Enzyme Kinetics and Docking Studies.
Yao Liu, João P G L M Rodrigues, Alexandre M J J Bonvin, Esther A Zaal, Celia R Berkers

J Biol Chem· July 2016

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A Machine Learning Approach for Hot-Spot Detection at Protein-Protein Interfaces.
Rita Melo, Robert Fieldhouse, André Melo, João D G Correia, Maria Natália D S Cordeiro, Alexandre M J J Bonvin

Int J Mol Sci· July 2016

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Structure-Function Relationships of Antimicrobial Peptides and Proteins with Respect to Contact Molecules on Pathogen Surfaces.
Ruiyan Zhang, Thomas Eckert, Thomas Lutteke, Stefan Hanstein, Axel Scheidig, Alexandre M J J Bonvin

Curr Top Med Chem· June 2016

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Data publication with the structural biology data grid supports live analysis.
Peter A Meyer, Stephanie Socias, Jason Key, Elizabeth Ransey, Emily C Tjon, Alexandre M J J Bonvin

Nat Commun· March 2016

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The solution structure of the kallikrein-related peptidases inhibitor SPINK6.
Sascha Jung, Jan Fischer, Björn Spudy, Tim Kerkow, Frank D Sönnichsen, Alexandre M J J Bonvin

Biochem Biophys Res Commun· February 2016

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Combination of Ambiguous and Unambiguous Data in the Restraint-driven Docking of Flexible Peptides with HADDOCK: The Binding of the Spider Toxin PcTx1 to the Acid Sensing Ion Channel (ASIC) 1a.
Evelyne Deplazes, Josephine Davies, Alexandre M J J Bonvin, Glenn F King, Alan E Mark

J Chem Inf Model· January 2016

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Editorial overview: Protein-protein interactions.
Alexandre M J J Bonvin, Özlem Keskin

Curr Opin Struct Biol· December 2015

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Novel Insights into Guide RNA 5'-Nucleoside/Tide Binding by Human Argonaute 2.
Munishikha Kalia, Sarah Willkomm, Jens Christian Claussen, Tobias Restle, Alexandre M J J Bonvin

Int J Mol Sci· December 2015

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Computational prediction of protein interfaces: A review of data driven methods.
Li C Xue, Drena Dobbs, Alexandre M J J Bonvin, Vasant Honavar

FEBS Lett· November 2015

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Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2.
Thom Vreven, Iain H Moal, Anna Vangone, Brian G Pierce, Panagiotis L Kastritis, Alexandre M J J Bonvin

J Mol Biol· September 2015

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Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop.
Andrej Sali, Helen M Berman, Torsten Schwede, Jill Trewhella, Gerard Kleywegt, Alexandre M J J Bonvin

Structure· July 2015

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Future opportunities and trends for e-infrastructures and life sciences: going beyond the grid to enable life science data analysis.
Afonso M S Duarte, Fotis E Psomopoulos, Christophe Blanchet, Alexandre M J J Bonvin, Manuel Corpas

Front Genet· July 2015

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Contacts-based prediction of binding affinity in protein-protein complexes.
Anna Vangone, Alexandre Mjj Bonvin

Elife· July 2015

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